SoroushVahidi/scidocs huggingface dataset:
Parametric and nonparametric linkage analysis: a unified multipoint approach.
(1996)

In complex disease studies, it is crucial to perform multipoint linkage analysis with many markers and to use robust nonparametric methods that take account of all pedigree information. Currently available methods fall short in both regards. In this paper, we describe how to extract complete multipoint inheritance information from general pedigrees of moderate size. This information is captured in the multipoint inheritance distribution, which provides a framework for a unified approach to both parametric and nonparametric methods of linkage analysis. Specifically, the approach includes the following: (1) Rapid exact computation of multipoint LOD scores involving dozens of highly polymorphic markers, even in the presence of loops and missing data. (2) Non-parametric linkage (NPL) analysis, a powerful new approach to pedigree analysis. We show that NPL is robust to uncertainty about mode of inheritance, is much more powerful than commonly used nonparametric methods, and loses little power relative to parametric linkage analysis. NPL thus appears to be the method of choice for pedigree studies of complex traits. (3) Information-content mapping, which measures the fraction of the total inheritance information extracted by the available marker data and points out the regions in which typing additional markers is most useful. (4) Maximum-likelihood reconstruction of many-marker haplotypes, even in pedigrees with missing data. We have implemented NPL analysis, LOD-score computation, information-content mapping, and haplotype reconstruction in a new computer package, GENEHUNTER. The package allows efficient multipoint analysis of pedigree data to be performed rapidly in a single user-friendly environment.
Extensions of Parallel Coordinates for Interactive Exploration of Large Multi-Timepoint Data Sets
(2008)

Parallel coordinate plots (PCPs) are commonly used in information visualization to provide insight into multi-variate data. These plots help to spot correlations between variables. PCPs have been successfully applied to unstructured datasets up to a few millions of points. In this paper, we present techniques to enhance the usability of PCPs for the exploration of large, multi-timepoint volumetric data sets, containing tens of millions of points per timestep. The main difficulties that arise when applying PCPs to large numbers of data points are visual clutter and slow performance, making interactive exploration infeasible. Moreover, the spatial context of the volumetric data is usually lost. We describe techniques for preprocessing using data quantization and compression, and for fast GPU-based rendering of PCPs using joint density distributions for each pair of consecutive variables, resulting in a smooth, continuous visualization. Also, fast brushing techniques are proposed for interactive data selection in multiple linked views, including a 3D spatial volume view. These techniques have been successfully applied to three large data sets: Hurricane Isabel (Vis'04 contest), the ionization front instability data set (Vis'08 design contest), and data from a large-eddy simulation of cumulus clouds. With these data, we show how PCPs can be extended to successfully visualize and interactively explore multi-timepoint volumetric datasets with an order of magnitude more data points.
Curved Folded Plate Timber Structures
(2011)

Current research at the laboratory for timber construction IBOIS at EPFL focuses on shell structures. Two main families are investigated: shells made of linear elements, as timber rib shells, and shells made of surface elements, typically folded plate structures. With regard to timber rib shells, bent linear timber elements are used to create the shape of a shell. With folded plate structures, new timber derived products are used to create structures made of planar panels, where the panel simultaneously covers space and acts as load bearing element. Indeed, timber industry has developed in the last fifteen years new large-size timber panels. Composition and dimensions of these panels and the possibility of milling them with Computer Numerical Controlled machines shows great potential for folded plate structures. In the present paper we investigate to combine both approaches using bent timber panels for curved folded plate structures.
Food region segmentation in meal images using touch points
(2012)

We propose an interactive scheme for segmenting meal images for automated dietary assessment. A smartphone user photographs a meal and marks a few touch points on the resulting image. The segmentation algorithm initializes a set of food segments with the touch points, and grows them using local image features. We evaluate the algorithm with a data set consisting of 300 manually segmented meal images. The precision of segmentation is 0.87, compared with 0.70 for fully automatic segmentation. The results show that the precision of segmentation was significantly improved by incorporating minimal user intervention.
Recurrent Capsule Network for Relations Extraction: A Practical Application to the Severity Classification of Coronary Artery Disease
(2018)

Coronary artery disease (CAD) is one of the leading causes of cardiovascular disease deaths. CAD condition progresses rapidly, if not diagnosed and treated at an early stage may eventually lead to an irreversible state of the heart muscle death. Invasive coronary arteriography is the gold standard technique for CAD diagnosis. Coronary arteriography texts describe which part has stenosis and how much stenosis is in details. It is crucial to conduct the severity classification of CAD. In this paper, we propose a recurrent capsule network (RCN) to extract semantic relations between clinical named entities in Chinese coronary arteriography texts, through which we can automatically find out the maximal stenosis for each lumen to inference how severe CAD is according to the improved method of Gensini. Experimental results on the corpus collected from Shanghai Shuguang Hospital show that our proposed RCN model achieves a F1-score of 0.9641 in relation extraction, which outperforms the baseline methods.
A Novel User Authentication Scheme Based on QR-Code
(2010)

User authentication is one of the fundamental procedures to ensure secure communications and share system resources over an insecure public network channel. Thus, a simple and efficient authentication mechanism is required for securing the network system in the real environment. In general, the password-based authentication mechanism provides the basic capability to prevent unauthorized access. Especially, the purpose of the one-time password is to make it more difficult to gain unauthorized access to restricted resources. Instead of using the password file as conventional authentication systems, many researchers have devoted to implement various one-time password schemes using smart cards, time-synchronized token or short message service in order to reduce the risk of tampering and maintenance cost. However, these schemes are impractical because of the far from ubiquitous hardware devices or the infrastructure requirements. To remedy these weaknesses, the attraction of the QR-code technique can be introduced into our one-time password authentication protocol. Not the same as before, the proposed scheme based on QR code not only eliminates the usage of the password verification table, but also is a cost effective solution since most internet users already have mobile phones. For this reason, instead of carrying around a separate hardware token for each security domain, the superiority of handiness benefit from the mobile phone makes our approach more practical and convenient.
Knowledge manipulation activities: results of a Delphi study
(2002)

Knowledge-based organizations are hosts for multitudes of knowledge management (KM) episodes. Each episode is triggered by a knowledge need and culminates with the satisfaction of that need (or its abandonment). Within an episode, one or more of the organization’ processors (human and/or computer-based) manipulate knowledge resources in various ways in an effort to meet the need. This paper identifies and characterizes a generic set of elemental knowledge manipulation activities that can be arranged in a variety of patterns within KM episodes. It also indicates possible knowledge flows that can occur among the activities. This descriptive framework was developed using conceptual synthesis and a Delphi methodology involving an international panel of researchers and practitioners in the KM field. The framework can serve as a common language for discourse about knowledge manipulation. For researchers, it suggests issues that deserve investigation and concepts that must be considered in explorations of KM episodes. For practitioners, the framework provides a perspective on activities that need to be considered in the design, measurement, control, coordination, and support of an organization’ KM episodes. # 2002 Elsevier Science B.V. All rights reserved.
Brain activities associated with gaming urge of online gaming addiction.
(2009)

The aim of this study was to identify the neural substrates of online gaming addiction through evaluation of the brain areas associated with the cue-induced gaming urge. Ten participants with online gaming addiction and 10 control subjects without online gaming addiction were tested. They were presented with gaming pictures and the paired mosaic pictures while undergoing functional magnetic resonance imaging (fMRI) scanning. The contrast in blood-oxygen-level dependent (BOLD) signals when viewing gaming pictures and when viewing mosaic pictures was calculated with the SPM2 software to evaluate the brain activations. Right orbitofrontal cortex, right nucleus accumbens, bilateral anterior cingulate and medial frontal cortex, right dorsolateral prefrontal cortex, and right caudate nucleus were activated in the addicted group in contrast to the control group. The activation of the region-of-interest (ROI) defined by the above brain areas was positively correlated with self-reported gaming urge and recalling of gaming experience provoked by the WOW pictures. The results demonstrate that the neural substrate of cue-induced gaming urge/craving in online gaming addiction is similar to that of the cue-induced craving in substance dependence. The above-mentioned brain regions have been reported to contribute to the craving in substance dependence, and here we show that the same areas were involved in online gaming urge/craving. Thus, the results suggest that the gaming urge/craving in online gaming addiction and craving in substance dependence might share the same neurobiological mechanism.
Enhancing well-being and alleviating depressive symptoms with positive psychology interventions: a practice-friendly meta-analysis.
(2009)

Do positive psychology interventions-that is, treatment methods or intentional activities aimed at cultivating positive feelings, positive behaviors, or positive cognitions-enhance well-being and ameliorate depressive symptoms? A meta-analysis of 51 such interventions with 4,266 individuals was conducted to address this question and to provide practical guidance to clinicians. The results revealed that positive psychology interventions do indeed significantly enhance well-being (mean r=.29) and decrease depressive symptoms (mean r=.31). In addition, several factors were found to impact the effectiveness of positive psychology interventions, including the depression status, self-selection, and age of participants, as well as the format and duration of the interventions. Accordingly, clinicians should be encouraged to incorporate positive psychology techniques into their clinical work, particularly for treating clients who are depressed, relatively older, or highly motivated to improve. Our findings also suggest that clinicians would do well to deliver positive psychology interventions as individual (versus group) therapy and for relatively longer periods of time.
ARLearn: Augmented Reality Meets Augmented Virtuality
(2012)

This article deals with educational opportunities for mixed reality games and related scenarios for learning. It discusses several issues and educational challenges to be tackled when linking augmented reality and augmented virtuality. Second, the paper describes the architecture of the ARLearn system which offers highly flexible support for different educational settings. Three prototypical use cases implemented based on the underlying ARLearn framework are discussed, which are a field trip system, an augmented Google StreetView client called StreetLearn, and a real time crisis intervention game. ARLearn combines real time notification and mixed reality games across Mobile Augmented Reality and Virtual Reality and the authors aim to use the underlying (open source) framework for further case studies and mixed reality applications for learning support.
High-quality computational imaging through simple lenses
(2013)

Modern imaging optics are highly complex systems consisting of up to two dozen individual optical elements. This complexity is required in order to compensate for the geometric and chromatic aberrations of a single lens, including geometric distortion, field curvature, wavelength-dependent blur, and color fringing.
 In this article, we propose a set of computational photography techniques that remove these artifacts, and thus allow for postcapture correction of images captured through uncompensated, simple optics which are lighter and significantly less expensive. Specifically, we estimate per-channel, spatially varying point spread functions, and perform nonblind deconvolution with a novel cross-channel term that is designed to specifically eliminate color fringing.
Feature vector selection and projection using kernels
(2003)

This paper provides new insight into kernel methods by using data selection. The kernel trick is used to select from the data a relevant subset forming a basis in a feature space F . Thus the selected vectors de,ne a subspace in F . Then, the data is projected onto this subspace where classical algorithms are applied. We show that kernel methods like generalized discriminant analysis (Neural Comput. 12 (2000) 2385) or kernel principal component analysis (Neural Comput. 10 (1998) 1299) can be expressed more easily. Moreover, it will turn out that the size of the basis is related to the complexity of the model. Therefore, the data selection leads to a complexity control and thus to a better generalization. The approach covers a wide range of algorithms. We investigate the function approximation on real classi,cation problems and on a regression problem. c © 2003 Elsevier B.V. All rights reserved.
A case for stateful forwarding plane
(2013)

In Named Data Networking (NDN), packets carry data names instead of source and destination addresses. This paradigm shift leads to a new network forwarding plane: data consumers send Interest packets to request desired data, routers forward Interest packets and maintain the state of all pending Interests, which is then used to guide Data packets back to the consumers. Maintaining the pending Interest state, together with the two-way Interest and Data exchange, enables NDN routers’ forwarding process to measure performance of different paths, quickly detect failures and retry alternative paths. In this paper we describe an initial design of NDN’s forwarding plane and evaluate its data delivery performance under adverse conditions. Our results show that this stateful forwarding plane can successfully circumvent prefix hijackers, avoid failed links, and utilize multiple paths to mitigate congestion. We also compare NDN’s performance with that of IP-based solutions to highlight the advantages of a stateful forwarding plane. 2013 Elsevier B.V. All rights reserved.
An ontology-based approach for the reconstruction and analysis of digital incidents timelines
(2015)

Due to the democratisation of new technologies, computer forensics investigators have to deal with volumes of data which are becoming increasingly large and heterogeneous. Indeed, in a single machine, hundred of events occur per minute, produced and logged by the operating system and various software. Therefore, the identification of evidence, and more generally, the reconstruction of past events is a tedious and time-consuming task for the investigators. Our work aims at reconstructing and analysing automatically the events related to a digital incident, while respecting legal requirements. To tackle those three main problems (volume, heterogeneity and legal requirements), we identify seven necessary criteria that an efficient reconstruction tool must meet to address these challenges. This paper introduces an approach based on a three-layered ontology, called ORD2I, to represent any digital events. ORD2I is associated with a set of operators to analyse the resulting timeline and to ensure the reproducibility of the investigation. © 2015 Elsevier Ltd. All rights reserved.
Assessing heterogeneity in meta-analysis: Q statistic or I2 index?
(2006)

In meta-analysis, the usual way of assessing whether a set of single studies is homogeneous is by means of the Q test. However, the Q test only informs meta-analysts about the presence versus the absence of heterogeneity, but it does not report on the extent of such heterogeneity. Recently, the I(2) index has been proposed to quantify the degree of heterogeneity in a meta-analysis. In this article, the performances of the Q test and the confidence interval around the I(2) index are compared by means of a Monte Carlo simulation. The results show the utility of the I(2) index as a complement to the Q test, although it has the same problems of power with a small number of studies.
BloomFlash: Bloom Filter on Flash-Based Storage
(2011)

The bloom filter is a probabilistic data structure that provides a compact representation of a set of elements. To keep false positive probabilities low, the size of the bloom filter must be dimensioned a priori to be linear in the maximum number of keys inserted, with the linearity constant ranging typically from one to few bytes. A bloom filter is most commonly used as an in memory data structure, hence its size is limited by the availability of RAM space on the machine. As datasets have grown over time to Internet scale, so have the RAM space requirements of bloom filters. If sufficient RAM space is not available, we advocate that flash memory may serve as a suitable medium for storing bloom filters, since it is about one-tenth the cost of RAM per GB while still providing access times orders of magnitude faster than hard disk. We present BLOOMFLASH, a bloom filter designed for flash memory based storage, that provides a new dimension of trade off with bloom filter access times to reduce RAM space usage (and hence system cost). The simple design of a single flat bloom filter on flash suffers from many performance bottlenecks, including in-place bit updates that are inefficient on flash and multiple reads and random writes spread out across many flash pages for a single lookup or insert operation. To mitigate these performance bottlenecks, BLOOMFLASH leverages two key design innovations: (i) buffering bit updates in RAM and applying them in bulk to flash that helps to reduce random writes to flash, and (ii) a hierarchical bloom filter design consisting of component bloom filters, stored one per flash page, that helps to localize reads and writes on flash. We use two real-world data traces taken from representative bloom filter applications to drive and evaluate our design. BLOOMFLASH achieves bloom filter access times in the range of few tens of microseconds, thus allowing up to order of tens of thousands operations per sec.
Optimizing the Hadoop MapReduce Framework with high-performance storage devices
(2015)

Solid-state drives (SSDs) are an attractive alternative to hard disk drives (HDDs) to accelerate the Hadoop MapReduce Framework. However, the SSD characteristics and today’s Hadoop framework exhibit mismatches that impede indiscriminate SSD integration. This paper explores how to optimize a Hadoop MapReduce Framework with SSDs in terms of performance, cost, and energy consumption. It identifies extensible best practices that can exploit SSD benefits within Hadoop when combined with high network bandwidth and increased parallel storage access. Our Terasort benchmark results demonstrate that Hadoop currently does not sufficiently exploit SSD throughput. Hence, using faster SSDs in Hadoop does not enhance its performance. We show that SSDs presently deliver significant efficiency when storing intermediate Hadoop data, leaving HDDs for Hadoop Distributed File System (HDFS). The proposed configuration is optimized with the JVM reuse option and frequent heartbeat interval option. Moreover, we examined the performance of a state-of-the-art non-volatile memory express interface SSD within the Hadoop MapReduce Framework. While HDFS read and write throughput increases with high-performance SSDs, achieving complete system performance improvement requires carefully balancing CPU, network, and storage resource capabilities at a system level.
HoPE: Hot-Cacheline Prediction for Dynamic Early Decompression in Compressed LLCs
(2017)

Data compression plays a pivotal role in improving system performance and reducing energy consumption, because it increases the logical effective capacity of a compressed memory system without physically increasing the memory size. However, data compression techniques incur some cost, such as non-negligible compression and decompression overhead. This overhead becomes more severe if compression is used in the cache. In this article, we aim to minimize the read-hit decompression penalty in compressed Last-Level Caches (LLCs) by speculatively decompressing frequently used cachelines. To this end, we propose a Hot-cacheline Prediction and Early decompression (HoPE) mechanism that consists of three synergistic techniques: Hot-cacheline Prediction (HP), Early Decompression (ED), and Hit-history-based Insertion (HBI). HP and HBI efficiently identify the hot compressed cachelines, while ED selectively decompresses hot cachelines, based on their size information. Unlike previous approaches, the HoPE framework considers the performance balance/tradeoff between the increased effective cache capacity and the decompression penalty. To evaluate the effectiveness of the proposed HoPE mechanism, we run extensive simulations on memory traces obtained from multi-threaded benchmarks running on a full-system simulation framework. We observe significant performance improvements over compressed cache schemes employing the conventional Least-Recently Used (LRU) replacement policy, the Dynamic Re-Reference Interval Prediction (DRRIP) scheme, and the Effective Capacity Maximizer (ECM) compressed cache management mechanism. Specifically, HoPE exhibits system performance improvements of approximately 11%, on average, over LRU, 8% over DRRIP, and 7% over ECM by reducing the read-hit decompression penalty by around 65%, over a wide range of applications.